[gmx-users] hdb file
Moeed
lecielll at googlemail.com
Thu Jul 1 23:12:52 CEST 2010
Dear Justin,
Thanks so much for your help. The structure looks almost fine now.
1-I am getting bond distance of 1.52 or 1.53 and angles of 112.2 / 112.0
with -d 0.0584/ 0.0581. Actually when I open up the same structure file in
VMD at different times I see even a little difference in bond distance
between atoms *on* the 4C unit chain (1.54 , 1.53 A). Thats why I though
maybe 1 or 2 degrees difference from equilibrium value of 110 for connecting
atoms does not influence results..But still I wanted to make sure if I need
to do energy minimization to get exact value of 110 for angles between
repeating units and if this is going to affect simulation results?
2- I am trying to obtain top and gro file including H atoms with hdb abd rtp
files. I am not getting any error messages and it seems everything is going
well but the gro file after adding H s has a very weird structure. I doubt I
have wriiten hdb file correctly. Could you please take a look at it?
editconf -f 4C.gro -o 4Cd.gro -princ -d 0.0584 -bt cubic
4Cd.gro
Great Red Owns Many ACres of Sand
4
1Eth C1 1 0.445 0.268 0.252
1Eth C2 2 0.308 0.199 0.252
1Eth C3 3 0.196 0.304 0.252
1Eth C4 4 0.058 0.238 0.252
0.50416 0.50416 0.50416
editconf -f 4Cd.gro -o 4Cdindex.gro -n index.ndx -princ
Great Red Owns Many ACres of Sand
4
1Eth C1 1 0.446 0.286 0.252
1Eth C2 2 0.321 0.198 0.252
1Eth C3 3 0.195 0.286 0.252
1Eth C4 4 0.068 0.201 0.252
0.50416 0.50416 0.50416
genconf -f 4Cdindex.gro -o 4Cdindex-rep.gro -nbox 5 1 1
4Cdindex-rep: with residues renamed
20
1EthB C1 1 0.446 0.286 0.252 0.0000 0.0000 0.0000
1EthB C2 2 0.321 0.198 0.252 0.0000 0.0000 0.0000
1EthB C3 3 0.195 0.286 0.252 0.0000 0.0000 0.0000
1EthB C4 4 0.068 0.201 0.252 0.0000 0.0000 0.0000
2Eth C1 5 0.950 0.286 0.252 0.0000 0.0000 0.0000
2Eth C2 6 0.825 0.198 0.252 0.0000 0.0000 0.0000
2Eth C3 7 0.699 0.286 0.252 0.0000 0.0000 0.0000
2Eth C4 8 0.572 0.201 0.252 0.0000 0.0000 0.0000
3Eth C1 9 1.454 0.286 0.252 0.0000 0.0000 0.0000
3Eth C2 10 1.329 0.198 0.252 0.0000 0.0000 0.0000
3Eth C3 11 1.203 0.286 0.252 0.0000 0.0000 0.0000
3Eth C4 12 1.076 0.201 0.252 0.0000 0.0000 0.0000
4Eth C1 13 1.958 0.286 0.252 0.0000 0.0000 0.0000
4Eth C2 14 1.833 0.198 0.252 0.0000 0.0000 0.0000
4Eth C3 15 1.707 0.286 0.252 0.0000 0.0000 0.0000
4Eth C4 16 1.580 0.201 0.252 0.0000 0.0000 0.0000
5EthE C1 17 2.463 0.286 0.252 0.0000 0.0000 0.0000
5EthE C2 18 2.338 0.198 0.252 0.0000 0.0000 0.0000
5EthE C3 19 2.212 0.286 0.252 0.0000 0.0000 0.0000
5EthE C4 20 2.085 0.201 0.252 0.0000 0.0000 0.0000
2.52080 0.50416 0.50416
*with hdb file*
Eth 4
2 6 H1 C1 C2 -C4
2 6 H2 C2 C1 +C1
2 6 H3 C3 C2 +C1
2 6 H4 C4 C3 +C1
EthB 4
3 4 H1 C1 C2 +C1
2 6 H2 C2 C1 +C1
2 6 H3 C3 C2 +C1
2 6 H4 C4 C3 +C1
EthE 4
2 6 H1 C1 C2 -C4
2 6 H2 C2 C1 -C4
2 6 H3 C3 C2 -C4
3 4 H4 C4 C3 -C4
with rtp file:
; Polyethylene - this is an internal residue
[ Eth ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
[ bonds ]
C1 -C4
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 +C1
; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ EthB ]
[ atoms ]
C1 opls_135 -0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
[ bonds ]
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 +C1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
H43 opls_140 0.060 4
[ bonds ]
C1 -C4
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 H43
gro file generated by pdb2gmx: first few lines
62
1EthB C1 1 0.446 0.286 0.252
1EthB H11 2 0.419 0.382 0.252
1EthB H12 3 0.500 0.267 0.334
1EthB H13 4 0.500 0.267 0.170
1EthB C2 5 0.321 0.198 0.252
1EthB H21 6 0.265 0.185 0.170
1EthB H22 7 0.265 0.185 0.334
1EthB C3 8 0.195 0.286 0.252
1EthB H31 9 0.138 0.292 0.334
1EthB H32 10 0.138 0.292 0.170
1EthB C4 11 0.068 0.201 0.252
1EthB H41 12 0.011 0.191 0.170
1EthB H42 13 0.011 0.191 0.334
2Eth C1 14 0.950 0.286 0.252
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